Dr Hardip Patel
Areas of expertise
- Bioinformatics 060102
- Genomics 060408
- Gene Expression (Incl. Microarray And Other Genome Wide Approaches) 060405
- Genome Structure And Regulation 060407
- Molecular Evolution 060409
- Phylogeny And Comparative Analysis 060309
Available student projects
National Centre for Indigenous Genomics is established under the federal legislation to ensure genomics research addresses the equity gap in personalised medicine for Indigenous Australians. NCIG Collection consists of blood samples, historical records, and genomic data obtained from >7000 Indigenous Australians.
We prioritise following research topics and methods for NCIG research:
- studying large and small genetic variations within and between Indigenous communities to understand their implications in health and disease, and their evolutionary properties
- develop and use innovative computational biology and bioinformatics techniques to assemble genomes and detect variations using population scale genomic data
We work in a multidisciplinary collaborative network to create high quality genomic resources and data products for their use in basic and translational research and clinical applications. Our work is conducted under the leadership and governance of the NCIG Indigenous majority Board to ensure benefit for Indigenous Australians.
We have various research projects available in genomics, computational biology, and bioinformatics based on skills and experience levels of prospective students. Prospective research students will have the opportunity to work in a dynamic environment with access to high-calibre researchers in our national collaborative network.
I have co-supervised 15 students at PhD, Masters, Honours, and Research Projects level. Students have found their experience rewarding and gone on to pursue their aspirations as post-doctoral researchers, or higher studies in their fields of interest. I would like to welcome new students into our research group to pursue high quality research in Indigenous genomics.
Publications
- Zhang, X, Wagner, S, Holleley, C et al. 2022, 'Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 4, pp. 1-9.
- McCartney, A, Anderson, J, Liggins, L et al. 2022, 'Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 4, pp. 1-9.
- Jadhao, S, Hoy, W, Lee, S et al. 2022, 'The genomic landscape of blood groups in Indigenous Australians in remote communities', Transfusion, vol. 62, no. 5, pp. 1110ââ¬â1120.
- Shankar, A, Jadhao, S, Hoy, W et al. 2021, 'Pharmacogenomic analysis of a genetically distinct Indigenous population', Pharmacogenomics Journal, vol. 22, pp. 100ââ¬â108.
- Prabhakaran, D, Patel, H, Chandrika, S et al. 2021, 'Genomic attributes differ between Vibrio parahaemolyticus environmental and clinical isolates including pathotypes', Environmental Microbiology Reports, vol. 14, no. 3, pp. 365-375.
- Li, Y, Patel, H & Lin, Y 2021, 'Kmer2SNP: Reference-free SNP calling from raw reads based on matching', 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) , IEEE, United States, pp. 208-212.
- Waters, P, Patel, H, Ruiz-Herrera, A et al. 2021, 'Microchromosomes are building blocks of bird, reptile, and mammal chromosomes', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 45, pp. 1-11.
- Chu-Tan, J, Cioanca, V, Feng, Z et al. 2021, 'Functional microRNA targetome undergoes degeneration-induced shift in the retina', Molecular Neurodegeneration, vol. 16, no. 1.
- Acera Mateos, P, Balboa, R, Easteal, S et al. 2021, 'PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses', Scientific Reports, vol. 11, no. 1.
- McInerney, T, Fulton-Howard, B, Patterson, C et al. 2021, 'A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants', BMC Bioinformatics, vol. 22, no. 417.
- Easteal, S, Arkell, R, Balboa, R et al. 2020, 'Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data', American Journal of Human Genetics, vol. 107, no. 2, pp. 175-182.
- Easteal, S, Arkell, R, Balboa, R et al. 2020, 'Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data', American Journal of Human Genetics, vol. 107, no. 2, pp. 175-182.
- Capraro, A, O'Meally, D, Waters, S et al. 2020, 'MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)', Scientific Reports, vol. 10, no. 1.
- Hart, N, Lamb, T, Patel, H et al. 2020, 'Visual opsin diversity in sharks and rays', Molecular Biology and Evolution, vol. 37, no. 3, pp. 811-827.
- Capraro, A, O'Meally, D, Waters, S et al. 2019, 'Waking the sleeping dragon: Gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps', BMC Genomics, vol. 20, no. 1.
- Arcos-Burgos PhD, M, Velez Valbuena, J, Martinez, A et al. 2019, 'ADGRL3 (LPHN3) variants predict substance use disorder', Translational Psychiatry, vol. 9, no. 42, pp. 15pp.
- Arcos-Burgos, M, Velez, J, Martinez, A, Lidbury BA, et al 2019, 'ADGRL3 (LPHN3) variants predict substance use disorder', Translational Psychiatry, vol. 9, no. 42, pp. 15pp.
- Johnson, R, O' Meally, D, Chen, Z et al 2018, 'Adaptation and conservation insights from the koala genome', Nature Genetics, vol. 50, no. 8, pp. 1102-1111pp.
- Hsieh JF, Chuah A, Patel HR, Sandhu KS, Foley WJ, Külheim C. 2018, 'Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals', Phytopathology, vol. 108, no. 4, pp. 495-509.
- Lamb, T, Patel, H, Chuah, A et al 2018, 'Evolution of the shut-off steps of vertebrate phototransduction', Open Biology, vol. 8, 170232.
- Natoli R, Mason E, Jiao H, Chuah A, Patel HR, Fernando N, Valter K, Wells CA, Provis J, Rutar M 2018, 'Dynamic Interplay of Innate and Adaptive Immunity During Sterile Retinal Inflammation: Insights From the Transcriptome', Frontiers in Immunology, vol. 9, no. 1666, pp. 1-17pp.
- Urbarova, I, Patel, H, Foret, S, Karlsen B, Jørgensen, T, Hall-Spencer, J, Johansen, S, 2018, 'Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing', Genome Biology and Evolution, vol. 10, no. 2, pp. 410-426.
- Waters SA, Livernois AM, Patel H, O'Meally D, Craig JM, Graves JA, Suter CM, Waters PD, 2018, 'Landscape of DNA Methylation on the Marsupial X', Molecular Biology and Evolution, vol. 35, no. 2, pp. 431-439.
- O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlight novel therapeutic targets', Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, 2017, John Wiley & Sons Ltd., Australia, pp. 119-119.
- O'Brien, C, Patel, H, Freeman, T et al. 2017, 'Gene expression differences between Crohn's disease aphthous ulcers and healthy Peyer's patches highlights potential treatment strategies [meeting abstract]', 12th Congress of European Crohn's and Colitis Organisation, ECCO 2017, ed. Laurence J Egan, Oxford University Press, United Kingdom, pp. S470-S470.
- Velez Valbuena, J, Lopera, F, Falla, D et al. 2016, 'APOE*E2 allele delays age of onset in PSEN1 E280A Alzheimer's disease', Molecular Psychiatry, vol. 21, no. 7, pp. 916-924.
- Soetanto, R, Hynes, C, Patel, H et al. 2016, 'Role of miRNAs and alternative mRNA 3 '-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1859, no. 5, pp. 744-756.
- Velez Valbuena, J, Rivera, D, Mastronardi, C et al. 2016, 'A Mutation in DAOA Modifies the Age of Onset in PSEN1 E280A Alzheimer's Disease', Neural Plasticity, vol. 2016, pp. 9760314-9760314.
- Johar, A, Sarmiento-Monroy, J, Rojas-Villarraga, A et al. 2016, 'Definition of mutations in polyautoimmunity', Journal of Autoimmunity, vol. 72, pp. 65-72.
- Deakin, J, Edwards, M, Patel, H et al 2016, 'Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome', BMC Genomics, vol. 17, no. 1, pp. -.
- Lamb, T, Patel, H, Chuah, A et al 2016, 'Evolution of Vertebrate Phototransduction: Cascade Activation', Molecular Biology and Evolution, vol. 33, no. 8, pp. 2064-2087.
- Velez Valbuena, J, Lopera, F, Patel, H et al. 2016, 'Mutations modifying sporadic Alzheimer's disease age of onset', American Journal of Medical Genetics, Part B: Neuropsychiatric, vol. 171, no. 8, pp. 1116-1130.
- Mastronardi, C, Pillai, E, Pineda, D et al. 2016, 'Linkage and association analysis of ADHD endophenotypes in extended and multigenerational pedigrees from a genetic isolate', Molecular Psychiatry, vol. 21, no. 10, pp. 1434-1440.
- Galgamuwa Arachchige, R, Hardy, K, Dahlstrom, J et al 2016, 'Dichloroacetate Prevents Cisplatin-Induced Nephrotoxicity without Compromising Cisplatin Anticancer Properties', Journal of the American Society of Nephrology, vol. 27, no. 11, pp. 3331-3344.
- Galgamuwa Arachchige, R, Hardy, K, Dahlstrom, J et al 2016, 'Dichloroacetate Prevents Cisplatin-Induced Nephrotoxicity without Compromising Cisplatin Anticancer Properties', Journal of the American Society of Nephrology, vol. 27, no. 11, pp. 3331-3344.
- Perez-Bercoff, A, Papanicolaou, A, Ramsperger, M et al 2015, 'DRAFT GENOME OF AUSTRALIAN ENVIRONMENTAL STRAIN WM 09 24 OF THE OPPORTUNISTIC HUMAN PATHOGEN SCEDOSPORIUM AURANTIACUM', Genome Announcements, vol. 3, no. 1, pp. e01526-14.
- Johar, A, Mastronardi, C, Rojas-Villarraga, A et al. 2015, 'Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome', Journal of Translational Medicine, vol. 13, no. 173, pp. 173-173.
- Georges, A, Li, Q, Lian, J et al 2015, 'High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps', GigaScience, vol. 4, no. 45, pp. 1-10.
- Padovan, A, Patel, H, Chuah, A et al 2015, 'Transcriptome Sequencing of Two Phenotypic Mosaic Eucalyptus Trees Reveals Large Scale Transcriptome Re-Modelling', PLOS ONE (Public Library of Science), vol. 10, no. 5, pp. e0123226-e0123226.
- Johar, A, Anaya, J, Andrews, D et al. 2015, 'Candidate gene discovery in autoimmunity by using extreme phenotypes, next generation sequencing and whole exome capture', Autoimmunity Reviews, vol. 14, no. 3, pp. 204-209.
- Srivastava, M, Duan, G, Kershaw, NJ et al 2015, 'Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis.', Nature Communications, vol. 6, no. 6253.
- Clancy, JL, Patel, HR, Hussein, SMI et al 2014, 'Small RNA changes en route to distinct cellular states of induced pluripotency', Nature Communications, vol. 5, p. 5522.
- Hussein, SMI, Puri, MC, Tonge, PD et al 2014, 'Genome-wide characterization of the routes to pluripotency', Nature, vol. 516, no. 7530, pp. 198-206.
- Da Paz Filho, G, Boguszewski, M, Mastronardi, C et al. 2014, 'Whole Exome Sequencing of Extreme Morbid Obesity Patients: Translational Implications for Obesity and Related Disorders', GENES, vol. 5, no. 3, pp. 709-725.
- Li, R, Patel, H, Perriman, D et al 2014, 'MICRORNA PROFILING IN WEAR PARTICLE ASSOCIATED OSTEOLYSIS', Bone and Joint Journal, vol. 96-B, no. SUPP 11 43.
- Sibbritt, T, Patel, H & Preiss, T 2013, 'Mapping and significance of the mRNA methylome', Wiley Interdisciplinary Reviews: WIREs RNA, vol. 4, no. 4, pp. 397-422.
- Squires, J, Patel, H, Nousch, M et al 2012, 'Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA', Nucleic Acids Research, vol. 40, no. 11, pp. 5023-33.
- Humphreys, D, Clancy, J, Patel, H et al. 2012, 'Complexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function', PLoS ONE, vol. 7, no. 2, pp. 1-18.
- Renfree, M, Papenfuss, A, Deakin, J et al 2011, 'Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development', Genome Biology, vol. 12, no. 8, pp. R81-R81.
- Wang, C, Webley, L, Wei, K et al 2011, 'A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)', BMC Genetics, vol. 12, no. 72, pp. 1-16.
- O'Meally, D, Patel, H, Stiglec, R et al 2010, 'Non-homologous sex chromosomes of birds and snakes share repetitive sequences', Chromosome Research, vol. 18, no. 7, pp. 787-800.
- Patel, H, Delbridge, M & Graves, J 2010, 'Organization and Evolution of the Marsupial X Chromosome', in Janine E Deakin, Paul D Waters & Jennifer A Marshall Graves (ed.), Marsupial Genetics and Genomics, Springer, Dordrecht; London, pp. 151-171.
- O'Meally, D, Miller, H, Patel, H et al 2009, 'The First Cytogenetic Map of the Tuatara, Sphenodon punctatus', Cytogenetic and Genome Research, vol. 127, no. 2, pp. 213-223.
- Delbridge, M, Patel, H, Waters, P et al 2009, 'Does the human X contain a third evolutionary block: Origin of genes on human Xp11 and Xq28', Genome Research, vol. 19, no. 8, pp. 1350-1360.
Projects and Grants
Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.
- Indigenous telomere-2-telomere human reference genomes to enable discovery, translation and innovations (Primary Investigator)
- Developing a long-read nanopore sequencing platform for Indigenous genomics (Secondary Investigator)
- Australian Genomics Grant Program (Secondary Investigator)
- Identifying key modulators of inflammation as therapeutic targets for retinal degenerations (Secondary Investigator)
- The use of microRNA as novel therapeutic targets for reducing retinal inflammation and degeneration (Secondary Investigator)